By 3067 the Amber Lotus had been in service alongside her sister ships for some years,[3] although a fifth Inazuma-class corvette under construction at the Dieron shipyards in 3058 had either never entered service or had been destroyed in service to the Dragon.[1]

The Amber Lotus survived the Jihad, one of only two Inazuma-class ships to remain in service by 3079, and had been redeployed back to the Midway system, defending the last shipyards in the Combine capable of repairing and maintaining WarShips.[4]

The Amber Lotus was a casualty of the Second Combine-Dominion War. Preparing for an inevitable escalation in the conflict, KhanAletha Kabrinski responded to an intelligence windfall that identified the location of the Amber Lotus as well as the location of both of the Combine's secret mobile factories, the reconditioned WarShips DCS Yamato and DCS Ryū - the renamed Mount Niikita. Kabrinski launched a preemptive strike against the three WarShips, which were located in the uninhabited Bikini Atoll system; Kabrinski dispatched the Leviathan-class Rasalhague and six Stars of Pocket WarShips and fighter carriers transported by a small flotilla of JumpShips to hunt down and destroy the three Combine WarShips.[5]

Although the location of the Bikini Atoll system was a closely guarded secret, the Combine didn't realise that the system was known to the Ghost Bears from Star League-era records relating to mass driver testing in the system from 2720 onwards. The Rasalhague's task force arrived in the system on the 18th of December 3099; the Combine forces split up and attempted to flee, with the Ryū heading in one direction and the Amber Lotus and Yamato in another. The Dominion ships split up and chased down all three WarShips, destroying all three, as well as the three Okinawa-class DropShips attached to the Amber Lotus (the DCS Comforting Silence, DCS Heated Sword, and DCS Iijima's Pride) and their aerospace fighters. The Dominion forces went so far as to destroy all of the escape pods that launched, and the discovery of the wreckage in the system by the Kyushu-class frigate DCS Draconis Rift led to a dramatic escalation in the war. Whilst the wreckage of the Amber Lotus had been left in-system, the Dominion forces had deliberately accelerated the hulks of the Ryū and the Yamato into the corona of the local star, destroying them both utterly.[5] A black box recovered from the Amber Lotus contained a final message from the commanding officer of the Amber Lotus, Sho-shoEmanuel Inoue; that message was subsequently broadcast on a number of major Combine news agencies.[6]